Ecology of SARS-CoV-2 in the post-pandemic era
Authors: Yafei Meng, David M Irwin, Yongyi Shen
Journal: The Lancet Microbe (2022)

The outbreak of COVID-19, caused by SARS-CoV-2, has posed a severe threat to global public health. The omicron variant is less pathogenic and causes more asymptomatic infections, thus the emergency phase might have passed. Many governments are rolling back restrictions, and, as of Dec 19, 2022, there are 153 countries without any travel restrictions (data from Travel Off Path). However, the omicron variant shows a greater propensity for human-to-human transmission than previous variants and the wild-type strain. Furthermore, the incidence of infection is still high (7·9–18·9%) in humans who received the two RNA vaccines (BNT162b2 and mRNA-1273) or were naturally infected.1Chemaitelly H Ayoub HH AlMukdad S et al.Protection from previous natural infection compared with mRNA vaccination against SARS-CoV-2 infection and severe COVID-19 in Qatar: a retrospective cohort study.Lancet Microbe. 2022; 3: e944-e955Summary Full Text Full Text PDF PubMed Scopus (8) Google Scholar It seems that the disease will become endemic and will be characterised by a lower pathogenicity, but with higher transmission rates, leading to large infection and reinfection numbers in the post-pandemic era (endemic phase). The ecology of SARS-CoV-2 in the post-pandemic era needs attention. SARS-CoV-2 transmission and reverse transmission from humans to animals that are in close contact with humans, such as zoo animals (pumas, tigers, lions, and gorillas), fur-bearing animals (minks and ferrets), and pets (cats and dogs) has been widely reported.2Frazzini S Amadori M Turin L Riva F SARS CoV-2 infections in animals, two years into the pandemic.Arch Virol. 2022; (published online Oct 7.)https://doi.org/10.1007/S00705-022-05609-1Crossref PubMed Scopus (3) Google Scholar, 3Oude Munnink BB Sikkema RS Nieuwenhuijse DF et al.Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans.Science. 2021; 371: 172-177Crossref PubMed Scopus (600) Google Scholar The pet population is very large in industrialised nations, where a high proportion of households have pets. For example, 25·4% of households in the USA have cats (data from the American Veterinary Medical Association). Considering the intimate contact between pets and zoo animals with humans, especially the large number of pets, the circulation of SARS-CoV-2 in these animals should not be neglected (appendix). ACE2 is the receptor for SARS-CoV-2. Within carnivores, a very limited number of amino acid differences are present in the ACE2 protein sequence at key sites involved in its interaction with the SARS-CoV-2 spike protein (appendix). This suggests that other carnivores genetically related to cats, dogs, minks, and ferrets are also likely to be susceptible to SARS-CoV-2. Many small and medium-sized carnivores, such as foxes, coyotes, weasels, skunks, badgers, and raccoons, have successfully colonised urban and suburban areas, where they exhibit population densities higher than in rural and wild environments.4Bateman PW Fleming PA Big city life: carnivores in urban environments.J Zool. 2012; 287: 1-23Crossref Scopus (494) Google Scholar Their food resources include human refuse, synanthropic rodents and birds, pets, and livestock. These urban wild carnivores might form a bridge for the transmission of viruses between pets and other animals in the wild. Indeed, some wild animals, such as white-tailed deer, are sensitive to SARS-CoV-2.5Pickering B Lung O Maguire F et al.Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission.Nat Microbiol. 2022; 7: 2011-2024Crossref PubMed Scopus (42) Google Scholar The interactions between humans, their pets, and urban wildlife increase the risk of potential expansions of SARS-CoV-2 in other species of wildlife. The above discussion suggests that the ecology of SARS-CoV-2 could be more complex than for other zoonotic viruses (appendix). Infections in humans would facilitate frequent human–animal transmissions. Then, the virus could experience sustained evolution with adaptation to multiple species of animals that results in antigenicity changes before subsequent reverse transmission to humans. This would make disease control more difficult. Therefore, characterisation of SARS-CoV-2 ecology and greater levels of surveillance for infections in animals, especially pets, zoo animals, and urban and suburban wildlife, are imperative in the post-pandemic era. For US pet ownership statistics see https://www.avma.org/resources-tools/reports-statistics/us-pet-ownership-statisticsFor countries without any travel restrictions see https://www.traveloffpath.com/countries-without-any-travel-restrictions-or-entry-requirements/ For US pet ownership statistics see https://www.avma.org/resources-tools/reports-statistics/us-pet-ownership-statistics For countries without any travel restrictions see https://www.traveloffpath.com/countries-without-any-travel-restrictions-or-entry-requirements/ We declare no competing interests. This work was supported by the Guangdong Provincial Key R&D Program (2022B1111040001), the Guangdong Major Project of Basic and Applied Basic Research (2020B0301030007), and the Laboratory of Lingnan Modern Agriculture Project (NT2021007). Download .pdf (.15 MB) Help with pdf files Supplementary appendix Protection from previous natural infection compared with mRNA vaccination against SARS-CoV-2 infection and severe COVID-19 in Qatar: a retrospective cohort studyPrevious natural infection was associated with lower incidence of SARS-CoV-2 infection, regardless of the variant, than mRNA primary-series vaccination. Vaccination remains the safest and most optimal tool for protecting against infection and COVID-19-related hospitalisation and death, irrespective of previous infection status. Full-Text PDF Open Access